Variant report

Variant	rs11939629
Chromosome Location	chr4:129037493-129037494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:129035426..129037558-chr4:129040093..129043006,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11932481	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11935232	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17012926	0.97[AFR][1000 genomes]
rs17012942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17012954	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2126113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4487359	0.82[AFR][1000 genomes]
rs57297662	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57767415	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59664646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60096181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60995278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61373286	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61662075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6836536	1.00[AMR][1000 genomes]
rs6844291	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv879923	chr4:128554404-129068179	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1792644	chr4:128566686-129133826	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1795770	chr4:128566686-129145581	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv3416036	chr4:128782694-129133956	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1033701	chr4:128803159-129095018	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	esv1841203	chr4:128817558-129043809	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1029890	chr4:128828468-129041302	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv1018952	chr4:128850790-129082821	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	nsv595388	chr4:128853913-129084831	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv1019555	chr4:128901614-129088903	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	esv3390887	chr4:128932563-129207255	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	esv1792524	chr4:128983925-129133826	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
14	nsv879929	chr4:129029653-129142079	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128983800-129066600	Weak transcription	Esophagus	oesophagus
2	chr4:128983800-129066600	Weak transcription	Small Intestine	intestine
3	chr4:128992800-129038400	Weak transcription	Thymus	Thymus
4	chr4:128994200-129066400	Weak transcription	Brain Angular Gyrus	brain
5	chr4:128997000-129054200	Weak transcription	Right Ventricle	heart
6	chr4:129000200-129066600	Weak transcription	Colonic Mucosa	Colon
7	chr4:129003600-129078800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:129003800-129047800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr4:129003800-129056400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr4:129003800-129066400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:129007800-129076400	Weak transcription	Gastric	stomach
12	chr4:129014400-129051400	Weak transcription	Fetal Kidney	kidney
13	chr4:129014400-129066600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:129016600-129048200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:129018800-129083400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:129019600-129045600	Weak transcription	HSMMtube	muscle
17	chr4:129020200-129051600	Weak transcription	Psoas Muscle	Psoas
18	chr4:129020400-129076600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:129020400-129076600	Weak transcription	Pancreas	Pancrea
20	chr4:129020600-129045200	Weak transcription	Fetal Thymus	thymus
21	chr4:129020800-129066600	Weak transcription	Primary T cells from cord blood	blood
22	chr4:129021000-129043800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:129021400-129076400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:129021600-129044000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr4:129021600-129046800	Weak transcription	Fetal Brain Female	brain
26	chr4:129021800-129038600	Weak transcription	Lung	lung
27	chr4:129021800-129051600	Weak transcription	NHEK	skin
28	chr4:129022400-129066400	Weak transcription	Left Ventricle	heart
29	chr4:129023200-129062800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:129024800-129066600	Weak transcription	HSMM	muscle
31	chr4:129025800-129056200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:129025800-129066600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr4:129026000-129062800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:129026000-129066400	Weak transcription	Aorta	Aorta
35	chr4:129026600-129045200	Weak transcription	Fetal Intestine Large	intestine
36	chr4:129026600-129055400	Weak transcription	NH-A	brain
37	chr4:129026600-129066400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:129026600-129066600	Weak transcription	Fetal Lung	lung
39	chr4:129026800-129043600	Weak transcription	Ovary	ovary
40	chr4:129029400-129066200	Weak transcription	Brain Hippocampus Middle	brain
41	chr4:129029600-129042000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr4:129029600-129047800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr4:129029800-129043000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:129029800-129043400	Weak transcription	GM12878-XiMat	blood
45	chr4:129029800-129043600	Weak transcription	Primary B cells from cord blood	blood
46	chr4:129029800-129043600	Weak transcription	HepG2	liver
47	chr4:129029800-129045800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:129029800-129045800	Weak transcription	Adipose Nuclei	Adipose
49	chr4:129029800-129046000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:129029800-129066400	Weak transcription	Rectal Smooth Muscle	rectum

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